The Hilbert-Huang Transform was applied to the satellite-derived monthly surface chlorophyll-a data and monthly blended satellite wind products from September 1997 to April 2010 to examine temporal trends in these time series. Using this new approach, we found an overall increasing trend in both the surface chlorophyll-a concentration and surface wind speed averaged over the entire South China Sea. Chlorophyll-a concentration increased by 12% between September 1997 and September 2003, and then decreased by 3% by April 2010. Wind speed increased by 21% between September 1997 and December 2005, but then decreased by 11%. The increasing trends followed by a period of decrease in both chlorophyll-a and wind speed time series are likely driven by the El Niño Southern Oscillation signal. The biggest change occurred in the deep basin region where the area averaged chlorophyll-a concentration increased by 20% between 1997 and 2010. This trend was primarily attributed to a 19% increase of the surface area of waters with monthly averaged chlorophyll-a concentration greater than 0.2 mg m −3, called the high chlorophyll waters. The most pronounced change occurred in winter with the high chlorophyll surface area expanding from 56 to 64% of the South China Sea. Strong correlation between chlorophyll-a and wind speed in this region suggested that it is the enhanced wind-induced mixing in the winter that stimulates phytoplankton growth via increased vertical supply of nutrients. The obtained 13-year trends indicate that the physical-biological interactions also take place on inter-annual time scales in the South China Sea.